schrodinger.application.steps.docking module

schrodinger.application.steps.docking.glide_server_log_level(level: int)

A context manager sets the glide server log level to level.

class schrodinger.application.steps.docking.GlideSettings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

The glide_in_file input file should not have a LIGANDFILE keyword.

glide_grid_file: schrodinger.stepper.stepper.StepperFile

A parameter of the class.

glide_ref_ligand_file: schrodinger.stepper.stepper.StepperFile

A parameter of the class.

glide_in_file: schrodinger.stepper.stepper.StepperFile

A parameter of the class.

poses_per_lig: int

A parameter of the class.

glide_input_overrides: dict

A parameter of the class.

validate(step)

Validate the settings for use in step.

Parameters

step – stepper._BaseStep

Return type

list[TaskError or TaskWarning]

glide_grid_fileChanged

A pyqtSignal emitted by instances of the class.

glide_grid_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_in_fileChanged

A pyqtSignal emitted by instances of the class.

glide_in_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_input_overridesChanged

A pyqtSignal emitted by instances of the class.

glide_input_overridesReplaced

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

poses_per_ligChanged

A pyqtSignal emitted by instances of the class.

poses_per_ligReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.steps.docking.GlideDocker(*args, **kwargs)

Bases: schrodinger.application.steps.docking._MolDockerMixin, schrodinger.application.steps.basesteps.MolMapStep

Perform a glide docking step.

Only yields the original input molecule if at least 1 pose is found with a score less than or equal to the settings’ max_score.

Note: it is not the docked Mol in the ScoredMol that is yielded.

GLIDE_SERVER_START_TASK_CLASS

alias of schrodinger.application.steps.docking._GlideServerStartTask

class Settings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.steps.docking.GlideSettings

max_score: float

A parameter of the class.

glide_grid_fileChanged

A pyqtSignal emitted by instances of the class.

glide_grid_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_in_fileChanged

A pyqtSignal emitted by instances of the class.

glide_in_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_input_overridesChanged

A pyqtSignal emitted by instances of the class.

glide_input_overridesReplaced

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

max_scoreChanged

A pyqtSignal emitted by instances of the class.

max_scoreReplaced

A pyqtSignal emitted by instances of the class.

poses_per_ligChanged

A pyqtSignal emitted by instances of the class.

poses_per_ligReplaced

A pyqtSignal emitted by instances of the class.

mapFunction(mol)

class schrodinger.application.steps.docking.MaeGlideDocker(*args, **kwargs)

Bases: schrodinger.application.steps.docking._MolDockerMixin, schrodinger.application.steps.basesteps.MaeMapStep

Perform a glide docking step, yielding up to POSES_PER_LIG of the best scored pose for each input structure.

GLIDE_SERVER_START_TASK_CLASS

alias of schrodinger.application.steps.docking._GlideServerStartTask

class Settings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.steps.docking.GlideSettings

max_score: float

A parameter of the class.

glide_grid_fileChanged

A pyqtSignal emitted by instances of the class.

glide_grid_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_in_fileChanged

A pyqtSignal emitted by instances of the class.

glide_in_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_input_overridesChanged

A pyqtSignal emitted by instances of the class.

glide_input_overridesReplaced

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

max_scoreChanged

A pyqtSignal emitted by instances of the class.

max_scoreReplaced

A pyqtSignal emitted by instances of the class.

poses_per_ligChanged

A pyqtSignal emitted by instances of the class.

poses_per_ligReplaced

A pyqtSignal emitted by instances of the class.

mapFunction(struc)

class schrodinger.application.steps.docking.SmilesDockerSettings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.steps.docking.GlideSettings

arg_string: str

A parameter of the class.

ligprep_filter_file: schrodinger.stepper.stepper.StepperFile

A parameter of the class.

validate(step)

Validate the settings for use in step.

Parameters

step – stepper._BaseStep

Return type

list[TaskError or TaskWarning]

arg_stringChanged

A pyqtSignal emitted by instances of the class.

arg_stringReplaced

A pyqtSignal emitted by instances of the class.

glide_grid_fileChanged

A pyqtSignal emitted by instances of the class.

glide_grid_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_in_fileChanged

A pyqtSignal emitted by instances of the class.

glide_in_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_input_overridesChanged

A pyqtSignal emitted by instances of the class.

glide_input_overridesReplaced

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

ligprep_filter_fileChanged

A pyqtSignal emitted by instances of the class.

ligprep_filter_fileReplaced

A pyqtSignal emitted by instances of the class.

poses_per_ligChanged

A pyqtSignal emitted by instances of the class.

poses_per_ligReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.steps.docking.SmilesDocker(*args, **kwargs)

Bases: schrodinger.application.steps.docking._MolDockerMixin, schrodinger.application.steps.basesteps.MolMapStep

Perform a ligprep with glide docking step. This step will yield the molecules and their glide score value as ScoredMol objects only for molecules that had a score that is less than or equal to the max_score in the settings.

Since to ligprep may generate different tautomers the same molecule may be yielded more than once.

GLIDE_SERVER_START_TASK_CLASS

alias of schrodinger.application.steps.docking._SmilesGlideServerStartTask

class Settings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.steps.docking.SmilesDockerSettings

max_score: float

A parameter of the class.

arg_stringChanged

A pyqtSignal emitted by instances of the class.

arg_stringReplaced

A pyqtSignal emitted by instances of the class.

glide_grid_fileChanged

A pyqtSignal emitted by instances of the class.

glide_grid_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_in_fileChanged

A pyqtSignal emitted by instances of the class.

glide_in_fileReplaced

A pyqtSignal emitted by instances of the class.

glide_input_overridesChanged

A pyqtSignal emitted by instances of the class.

glide_input_overridesReplaced

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

glide_ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

ligprep_filter_fileChanged

A pyqtSignal emitted by instances of the class.

ligprep_filter_fileReplaced

A pyqtSignal emitted by instances of the class.

max_scoreChanged

A pyqtSignal emitted by instances of the class.

max_scoreReplaced

A pyqtSignal emitted by instances of the class.

poses_per_ligChanged

A pyqtSignal emitted by instances of the class.

poses_per_ligReplaced

A pyqtSignal emitted by instances of the class.

mapFunction(mol)